getMST: Create a MST from distance matrix

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Create a MST from distance matrix

Description

Builds a minimum spanning tree from the distance.

Usage

getMST(distMat)

Arguments

distMat

(dist) a pairwise distance matrix.

Value

(matrix) array of tree-edges.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-05-14

See Also

mst, traverseMST

Examples

m <- matrix(c(0,13,21,22, 13,0,12,13, 21,12,0,13, 22,13,13,0), byrow = TRUE,
            ncol = 4, dimnames = list(c("run1", "run2", "run3", "run4"),
                                      c("run1", "run2", "run3", "run4")))
distMat <- as.dist(m, diag = FALSE, upper = FALSE)
## Not run: 
x <- as.data.frame(getMST(distMat))
weights <- reshape2::melt(as.matrix(distMat))
weights$Var <- paste(weights$Var1, weights$Var2, sep = "_")
x$weight <- weights[match(paste(x[,1], x[,2], sep = "_"), weights$Var), "value"]
g1 <- igraph::graph_from_data_frame(x, directed = FALSE)
plot(g1, edge.label = igraph::E(g1)$weight)

## End(Not run)

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.